Introduction Methicillin-resistant Staphylococcus aureus (MRSA) causes severe morbidity and mortality in intensive care units (ICUs) worldwide. The purpose of this study was to determine whether intranasal mupirocin prophylaxis is useful to prevent ICU-acquired infections with MRSA. Materials and methods We conducted a 4-year observational retrospective study in a 15-bed adult medical ICU. During the first 2-year period mupirocin ointment was included in the MRSA control programme; during the second, mupirocin was not used. The main endpoint was the number of endogenous ICU-acquired infections with MRSA. Results The number of endogenous acquired infections was significantly higher during the second period than during the first (11 versus 1; P = 0.02), although there was no significant difference in the total number of patients infected with MRSA between the two periods. We also observed that nasal MRSA decolonisation was significantly higher in the mupirocin period than in mupirocin-free period (P = 0.002). Conclusion Our findings suggest that intranasal mupirocin can prevent endogenous acquired MRSA infection in an ICU. Further double-blind, randomised, placebo-controlled studies are needed to demonstrate its cost-effectiveness and its impact on resistance.